Hp XC System 2.x Software Uživatelský manuál Strana 21
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Hodnocené. / 5. Na základě hodnocení zákazníků
choose to use either the HP XC Administrative Network, or the XC system Interconnect, for
NFS operatio ns. The HP XC system interconnect can potentially offer h igh er p erforman ce, but
only at the potential expense of the performance of application communications.
For high-performance or high-availability file I/O, the L ust re file system is available on HP
XC. T he Lustre file system uses POSIX-compliant syntax and semantics. The HP XC System
Software includes kernel modifications required for Lustr e client services which enables the
operation of t he separately installable Lustre client software. The Lustre file server product used
on HP XC is the HP Storage Works Scalable File Share (SFS), which fully supports the HP XC.
The SFS includes HP XC Lustre client software. The SFS can be integrated with the HP XC so
that Lustre I/O is performed over the same high-speed system interconnect fabric used by the
HP XC. So, for example, if the HP XC system interconnect is based on a Quadrics QsNet II
switch, then the SFS will serve files over ports on that switch. The file operations are able to
proceed at the full b andwidth of the HP XC system interconnect because these operations are
implemented directly over the low- level communications libraries. Further optimizations of file
I/O can be achieved at the application level using special file system com mands – implemented
as ioctls – which allow a program to int err ogat e the attributes of the file system, modify the
stripe size and other attributes of new (zero-length) files, and so on. Some of these optimizations
are imp li cit in the HP- M PI I/O library, wh ich implements the MPI-2 file I/O standard.
File System Layout
In an HP XC system, the basic file system layout is the same as that o f the Red Hat Advanced
Server 3.0 Linux file system.
The HP XC file system is structured to separate cluster-specific files, base operating system
files, and user-installed software files. This allows f or flexibility and ease of potential upgrades
of the system software as well as keeping software from conflictin g with user installed software.
Files are segregated into the following types an d locations:
• HP XC-specific software is located in /opt/hptc
• HP XC configuratio n data is located in /opt/hptc/etc
• Clusterwide directory structure (file system) is located in /hptc_cluster
You should be aw a re of the following information about the H P XC file system layout:
• Open source software th at by default wo uld be installed u nder the /usr/local directory
is instead installed in the /opt/hptc directory.
• Software installed in the /opt/hptc directory is not intended to b e updated by users.
• Software packages are installed in directories under the /opt/hptc directory under their
own names. The exception to this is 3rd-party software, which usually goe s in /opt/r.
• There are four directories under the /opt/hptc directory that contain symbolic links
to files included in the packages:
- /opt/hptc/bin
- /opt/hptc/sbin
- /opt/hptc/lib
- /opt/hptc/man
Each package d irectory should have a directory corresponding to each of these directories
where every file has a symbolic link created in the /opt/hptc/ directory.
1.1.5 System Interconnect Network
The HP XC sy stem interconnect provides high-speed connectivity for parallel app lications. The
system interconnect network provides a high speed communications path used primarily for
user file service and for communications within user applications that are distributed among
Overview of the User Environment 1-3
- HP XC System Software 1
- Contents 3
- 3 Developing Applications 4
- 4 Debugging Applications 5
- 5 Tuning Applications 5
- 6UsingSLURM 5
- 8UsingHP-MPI 6
- 7 Using LSF 6
- 9UsingHPMLIB 7
- 10 Advanced Topics 8
- AExamples 8
- About This Document 11
- HP XC Inform ation 12
- For M ore Information 13
- Supplementary Information 13
- Manpages 14
- Related Information 15
- Typographical Conventions 16
- HP Encourages Your Comments 17
- 1.1 System Architecture 19
- 1.1.3 Storage and I/O 20
- 1.1.4 File System 20
- 1.2 User Environment 22
- 1.3.1 Parallel Applications 23
- 1.3.2 Serial Applications 23
- 1.4 Run-Time E nvironment 24
- 1.4.4 HP-MPI 25
- Using the System 27
- 2.2.1 Notes on Modulefiles 28
- 2.2.2 Supplied Modulefiles 29
- 2.2.6 Loading a Modulefile 30
- 2.2.7 Unloading a M odulefile 31
- 2.2.8 Modulefile Conflicts 31
- 2.2.9 Creating a Mod u lefile 32
- 2.3.1 Introduction 33
- 2.3.5 Launching Jobs 34
- $ man sinfo 39
- $ man -k keyword 39
- Using the System 2-13 39
- Developing Applications 41
- 3.2 Using Compilers 42
- 3.4 Interrupting a Job 43
- 3-4 Developing Applications 44
- Developing Applications 3-5 45
- 3-6 Developing Applications 46
- Developing Applications 3-7 47
- $ module load mpi 48
- $ mpicc -o mycode hello.c 48
- $ mpif90 -o mycode hello.f 48
- 3-8 Developing Applications 48
- 3.8 Developing Libraries 49
- 3.9 Advanced To pics 50
- 3-14 Deve loping Applications 54
- Developing Applications 3-15 55
- Debugging Applications 57
- 4-2 D ebugging Applications 58
- $ totalview 60
- 4-4 D ebugging Applications 60
- Debugging Applications 4-5 61
- 4-6 D ebugging Applications 62
- -verbosity %V %F" 63
- Debugging Applications 4-7 63
- 4-8 D ebugging Applications 64
- Etnus TotalView Version# 65
- Debugging Applications 4-9 65
- $ mpirun -srun -n2 Psimple 66
- 4-10 Debugging Applications 66
- $ squeue 67
- $ scancel --user username 67
- Debugging Applications 4-11 67
- Tuning Applications 69
- Using SLURM 71
- $ srun -N 16 -b myscript.sh 73
- $ srun -A -N 4 myscript.sh 73
- $ srun -a 6543 -j 73
- Using SLURM 6-3 73
- 6.4.2 srun Signal Handling 74
- 6.4.3 srun Run-Mode Options 74
- Using SLURM 6-5 75
- 6-6 Using SLURM 76
- 6.4.5 srun Control Options 77
- 6.4.6 srun I/O Options 78
- Using SLURM 6-9 79
- 6.4.7 srun Constraint Options 80
- Using SLURM 6-11 81
- 6.4.9 Using srun with HP-MPI 82
- 6.4.10 Using srun with LSF 82
- 6.8 Job Accounting 84
- 6.9 Fault Tolerance 84
- 6.10 Security 84
- Using LSF 85
- 7.1.2 Topology Support 86
- 7.1.3 Notes on LSF-HPC 87
- SLURM_JOBID=53 89
- SLURM_NPROCS=4 89
- 7-6 Using LSF 90
- 7.3.1 Getting Status of LSF 91
- $ bhosts 92
- 7-8 Using LSF 92
- 7.4 Submitting Jobs 93
- 7.4.3 Submitting a Serial Job 97
- Using LSF 7-17 101
- 7-18 Using LSF 102
- Using HP-MPI 111
- 8.3.3 Using srun with HP-MPI 114
- 8.3.4 Using LSF and HP-MPI 116
- 8.3.5 MPI Versioning 117
- 8.6 Truncated Messages 118
- 8.5 32-Bit B uilds on XC4000 118
- Using HP-MPI 8-9 119
- 8.9 Environment Variables 120
- 8.9.5 MPI_PIN_PERCENTAGE 121
- 8.9.6 MPI_PAGE_ALIGN_MEM 121
- 8.9.7 MPI_MAX_WINDOW 121
- 8.9.8 MPI_ELANLOCK 121
- 8.9.9 MPI_USE_LIBELAN 121
- 8.9.10 MPI_USE_LIBELAN_SUB 122
- Work-arounds 124
- Using HP MLIB 125
- 9.1.2 MLIB and Module Files 126
- 9.2.1 Platform Sup port 126
- 9.2.2 Library Support 126
- 9.2.3 MPI Parallelism 126
- 9.2.4 Modulefiles and MLIB 127
- 9.2.6 Compiling and Linking 127
- 9.2.7 Licensing 128
- 9.2.8 MLIB Man pages 128
- 9.3.1 Platform Sup port 128
- 9.3.2 Library Support 128
- 9.3.3 MPI Parallelism 129
- 9.3.4 Modulefiles and MLIB 129
- 9.3.5 Compiling and Linking 129
- 9.3.6 Licensing 130
- 9.3.7 MLIB Man pages 130
- Advanced Topics 131
- Examples 135
- $ lshosts 140
- Show the environment: 142
- Run the job: 142
- View the running job: 142
- View the finished job: 142
- Examples A-9 143
- Glossary 145
- Glossary-2 146
- Glossary-3 147
- Glossary-4 148
- Glossary-5 149
- Glossary-6 150
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